If you mean "in-game cutscenes" (using the game elements), I can't tell you (as I've never done them before) but I know it does involve the use of camera's in a level.

massassi.net and some other editing sites have tutorials on making them. They are sometimes referred to as "MOTS style cutscenes" (even though this term isn't quit correct, since there are "in-game" cutscenes in JK as well as MOTS).

The cutscenes from MOTS that play off of the CD (those low quality ones that are in that "letterbox" widescreen format) I don't think can be edited. I don't know of any programs that make them either. They are made in the same way as the in-game ones, but somehow converted to another format and then stored on the CD.

The JK cutscenes (the ones that play off of the CD, in Full Motion Video) are created using Smacker, (smacker video technology). You can download this program for free off of many editing sites, and edit and create smk files for cutscenes. I'm sure there are also Smacker tutorials around somewhere. I've only converted avi files using Smacker for cutscenes, I've never taken the time to make a really good one. ; )